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- PDB-5k7j: Structure of designed zinc binding protein ZE2 bound to Zn2+ -

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Basic information

Entry
Database: PDB / ID: 5k7j
TitleStructure of designed zinc binding protein ZE2 bound to Zn2+
ComponentsIndole-3-glycerol phosphate synthase
KeywordsMETAL BINDING PROTEIN / Metalloprotein / Designed / TIM barrel
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
AuthorsGuffy, S.L. / Der, B.S. / Kuhlman, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117968 United States
National Science Foundation (NSF, United States)CBET-1403663 United States
CitationJournal: Protein Eng.Des.Sel. / Year: 2016
Title: Probing the minimal determinants of zinc binding with computational protein design.
Authors: Guffy, S.L. / Der, B.S. / Kuhlman, B.
History
DepositionMay 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Indole-3-glycerol phosphate synthase
B: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0604
Polymers56,9302
Non-polymers1312
Water2,360131
1
A: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5302
Polymers28,4651
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5302
Polymers28,4651
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.718, 79.029, 74.077
Angle α, β, γ (deg.)90.000, 95.700, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer determined by size exclusion chromatography

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Components

#1: Protein Indole-3-glycerol phosphate synthase / IGPS


Mass: 28464.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Computationally designed zinc binding protein using PDB ID 1a53 as a starting scaffold.
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: trpC, SSO0895 / Plasmid: pQE-MBP
Details (production host): N-terminal maltose binding protein with 6-His tag and TEV cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q06121, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.10 M succinate 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.07426 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07426 Å / Relative weight: 1
ReflectionResolution: 1.39→73.71 Å / Num. obs: 91000 / % possible obs: 99.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 28.1
Reflection shellResolution: 1.39→1.4 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2.1 / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.62 Å
Translation2.5 Å28.62 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A53

1a53


Resolution: 1.39→28.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.071 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0678 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.072 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 4579 5 %RANDOM
Rwork0.196 ---
obs0.1977 86360 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.64 Å2 / Biso mean: 20.389 Å2 / Biso min: 7.63 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.39→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 2 131 3999
Biso mean--23.97 19.98 -
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0193976
X-RAY DIFFRACTIONr_angle_refined_deg2.4031.9885359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67723.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1315774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1431539
X-RAY DIFFRACTIONr_chiral_restr0.160.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212919
X-RAY DIFFRACTIONr_mcbond_it2.2381.7871946
X-RAY DIFFRACTIONr_mcangle_it3.2112.662426
X-RAY DIFFRACTIONr_scbond_it3.6712.1922030
LS refinement shellResolution: 1.388→1.424 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 215 -
Rwork0.249 3333 -
all-3548 -
obs--50 %

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